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#ifndef CODE_ParametersChimeric
#define CODE_ParametersChimeric
#include "IncludeDefine.h"
class Parameters;
class ParametersChimeric
{//
public:
uint segmentMin, junctionOverhangMin; //min chimeric donor/acceptor length
uint segmentReadGapMax; //max read gap for stitching chimeric windows
int scoreMin,scoreDropMax,scoreSeparation, scoreJunctionNonGTAG; //min chimeric score
uint mainSegmentMultNmax;
uint multimapScoreRange, multimapNmax, nonchimScoreDropMin;
vector<int> outJunctionFormat;
struct
{
vector <string> stringIn;
bool genomicN;
} filter;
struct
{
vector <string> type;
bool bam;
bool bamHardClip;
bool samOld;
bool junctions;
} out;
void initialize(Parameters *pPin);
private:
Parameters *pP;
};
#endif
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